
@article{caiImpactSoilClay2018,
  ids = {caiImpactSoilClay2018a},
  title = {Impact of Soil Clay Minerals on Growth, Biofilm Formation, and Virulence Gene Expression of {{Escherichia}} Coli {{O157}}:{{H7}}},
  shorttitle = {Impact of Soil Clay Minerals on Growth, Biofilm Formation, and Virulence Gene Expression of {{Escherichia}} Coli {{O157}}},
  author = {Cai, Peng and Liu, Xing and Ji, Dandan and Yang, Shanshan and Walker, Sharon L. and Wu, Yichao and Gao, Chunhui and Huang, Qiaoyun},
  year = {2018},
  month = dec,
  volume = {243},
  pages = {953--960},
  issn = {0269-7491},
  doi = {10.1016/j.envpol.2018.09.032},
  abstract = {Soil, composed mainly of minerals, plays a central role in the circulation of microbial pathogens in the environment. Herein, the growth, biofilm formation, and virulence gene expression of the pathogenic bacteria Escherichia coli O157:H7 were monitored following exposure to montmorillonite, kaolinite, and goethite, three common soil minerals in the clay size fraction. E.~coli O157:H7 growth was notably promoted (P {$<$} 0.05), while biofilm formation was inhibited in the presence of montmorillonite (P {$<$} 0.05), which is attributed to the suppression of colanic acid (CA) production and an increase in bacterial motility. Kaolinite not only promoted bacterial growth (P {$<$} 0.05), but also contributed to biofilm formation upon stimulating CA production. Upon exposure to goethite, notably slower bacterial growth and higher biomass of biofilm were observed as compared to the control (P {$<$} 0.05). Goethite stimulated the synthesis of CA to encase cells in a protective biofilm in response to the tight association between bacteria and goethite, which could cause bacterial death. Additionally, the transcription of virulence factors (stxA-1 and stxA-2) was significantly decreased in goethite or kaolinite system (P {$<$} 0.05). These findings indicate that minerals play important roles in the physiological state of bacteria and ultimately govern the fate of this pathogen in soils.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\2018\\Environmental Pollution\\Cai et al_2018_Impact of soil clay minerals on growth, biofilm formation, and virulence gene.pdf},
  journal = {Environmental Pollution},
  keywords = {课题6研究论文,课题6第一标注,课题6蔡鹏组},
  number = {B}
}

@article{caiSoilBiofilmsMicrobial2019,
  title = {Soil Biofilms: Microbial Interactions, Challenges, and Advanced Techniques for Ex-Situ Characterization},
  shorttitle = {Soil Biofilms},
  author = {Cai, Peng and Sun, Xiaojie and Wu, Yichao and Gao, Chunhui and Mortimer, Monika and Holden, Patricia A. and {Redmile-Gordon}, Marc and Huang, Qiaoyun},
  year = {2019},
  month = jul,
  volume = {1},
  pages = {85--93},
  issn = {2662-2297},
  doi = {10.1007/s42832-019-0017-7},
  abstract = {Soil is inhabited by a myriad of microorganisms, many of which can form supracellular structures, called biofilms, comprised of surface-associated microbial cells embedded in hydrated extracellular polymeric substance that facilitates adhesion and survival. Biofilms enable intensive inter- and intra-species interactions that can increase the degradation efficiency of soil organic matter and materials commonly regarded as toxins. Here, we first discuss organization, dynamics and properties of soil biofilms in the context of traditional approaches to probe the soil microbiome. Social interactions among bacteria, such as cooperation and competition, are discussed. We also summarize different biofilm cultivation devices in combination with optics and fluorescence microscopes as well as sequencing techniques for the study of soil biofilms. Microfluidic platforms, which can be applied to mimic the complex soil environment and study microbial behaviors at the microscale with high-throughput screening and novel measurements, are also highlighted. This review aims to highlight soil biofilm research in order to expand the current limited knowledge about soil microbiomes which until now has mostly ignored biofilms as a dominant growth form.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\2019\\Soil Ecology Letters\\Cai et al_2019_Soil biofilms.pdf},
  journal = {Soil Ecology Letters},
  keywords = {课题6研究论文,课题6蔡鹏组},
  language = {en},
  number = {3-4}
}

@article{caoIdentificationFunctionalStudy2016,
  title = {Identification and Functional Study of Type {{III}}-{{A CRISPR}}-{{Cas}} Systems in Clinical Isolates of {{Staphylococcus}} Aureus},
  author = {Cao, Linyan and Gao, Chun-Hui and Zhu, Jiade and Zhao, Liping and Wu, Qingfa and Li, Min and Sun, Baolin},
  year = {2016},
  month = dec,
  volume = {306},
  pages = {686--696},
  issn = {1438-4221},
  doi = {10.1016/j.ijmm.2016.08.005},
  abstract = {The CRISPR-Cas (clustered regularly interspaced short palindromic repeats [CRISPR]-CRISPR associated proteins [Cas]) system can provide prokaryote with immunity against invading mobile genetic elements (MGEs) such as phages and plasmids, which are the main sources of staphylococcal accessory genes. To date, only a few Staphylococcus aureus strains containing CRISPR-Cas systems have been identified, but no functional study in these strains has been reported. In this study, 6 clinical isolates of S. aureus with type III-A CRISPR-Cas systems were identified, and whole-genome sequencing and functional study were conducted subsequently. Genome sequence analysis revealed a close linkage between the CRISPR-Cas system and the staphylococcal cassette chromosome mec (SCCmec) element in five strains. Comparative sequence analysis showed that the type III-A repeats are conserved within staphylococci, despite of the decreased conservation in trailer-end repeats. Highly homologous sequences of some spacers were identified in staphylococcal MGEs, and partially complementary sequences of spacers were mostly found in the coding strand of lytic regions in staphylococcal phages. Transformation experiments showed that S. aureus type III-A CRISPR-Cas system can specifically prevent plasmid transfer in a transcription-dependent manner. Base paring between crRNA and target sequence, the endoribonuclease, and the Csm complex were proved to be necessary for type III-A CRISPR-Cas immunity.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\2016\\International Journal of Medical Microbiology\\Cao et al_2016_Identification and functional study of type III-A CRISPR-Cas systems in.pdf},
  journal = {International Journal of Medical Microbiology},
  number = {8}
}

@article{gaoCocultureSoilBiofilm2018,
  title = {Co-Culture of Soil Biofilm Isolates Enables the Discovery of Novel Antibiotics},
  author = {Gao, Chun-Hui and Cai, Peng and Li, Zhunjie and Wu, Yichao and Huang, Qiaoyun},
  year = {2018},
  month = jun,
  pages = {353755},
  doi = {10.1101/353755},
  abstract = {Bacterial natural products (NPs) are considered to be a promising source of drug discovery. However, the biosynthesis gene clusters (BGCs) of NP are not often expressed, making it difficult to identify them. Recently, the study of biofilm community showed bacteria may gain competitive advantages by the secretion of antibiotics, implying a possible way to screen antibiotic by evaluating the social behavior of bacteria. In this study, we have described an efficient workflow for novel antibiotic discovery by employing the bacterial social interaction strategy with biofilm cultivation, co-culture, transcriptomic and genomic methods. We showed that a biofilm dominant species, i.e. Pseudomonas sp. G7, which was isolated from cultivated soil biofilm community, was highly competitive in four-species biofilm communities, as the synergistic combinations preferred to exclude this strain while the antagonistic combinations did not. Through the analysis of transcriptomic changes in four-species co-culture and the complete genome of Pseudomonas sp. G7, we finally discovered two novel non-ribosomal polypeptide synthetic (NRPS) BGCs, whose products were predicted to have seven and six amino acid components, respectively. Furthermore, we provide evidence showing that only when Pseudomonas sp. G7 was co-cultivated with at least two or three other bacterial species can these BGC genes be induced, suggesting that the co-culture of the soil biofilm isolates is critical to the discovery of novel antibiotics. As a conclusion, we set a model of applying microbial interaction to the discovery of new antibiotics.},
  copyright = {\textcopyright{} 2018, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), CC BY-NC 4.0, as described at http://creativecommons.org/licenses/by-nc/4.0/},
  file = {E\:\\zotero.storage.2016\\2018\\bioRxiv\\Gao et al_2018_Co-culture of soil biofilm isolates enables the discovery of novel antibiotics.pdf},
  journal = {bioRxiv},
  keywords = {课题6研究论文,课题6第一标注,课题6蔡鹏组,高春辉一作或通讯论文},
  language = {en}
}

@article{guoDissectingTranscriptionRegulatory2009,
  title = {Dissecting Transcription Regulatory Pathways through a New Bacterial One-Hybrid Reporter System},
  author = {Guo, Manman and Feng, Hui and Zhang, Jun and Wang, Wenqin and Wang, Yi and Li, Yuqing and Gao, Chunhui and Chen, Huanchun and Feng, Ying and He, Zheng-Guo},
  year = {2009},
  month = jul,
  volume = {19},
  pages = {1301--1308},
  issn = {1088-9051},
  doi = {10.1101/gr.086595.108},
  abstract = {Sequence-specific DNA-binding transcription factors have widespread biological significance in the regulation of gene expression. However, in lower prokaryotes and eukaryotic metazoans, it is usually difficult to find transcription regulatory factors that recognize specific target promoters. To address this, we have developed in this study a new bacterial one-hybrid reporter vector system that provides a convenient and rapid strategy to determine the specific interaction between target DNA sequences and their transcription factors. Using this system, we have successfully determined the DNA-binding specificity of the transcription regulator Rv3133c to a previously reported promoter region of the gene Rv2031 in Mycobacterium tuberculosis. In addition, we have tested more than 20 promoter regions of M. tuberculosis genes using this approach to determine if they interact with approximately 150 putative regulatory proteins. A variety of transcription factors are found to participate in the regulation of stress response and fatty acid metabolism, both of which comprise the core of in vivo-induced genes when M. tuberculosis invades macrophages. Interestingly, among the many new discovered potential transcription factors, the WhiB-like transcriptional factor WhiB3 was identified for the first time to bind with the promoter sequences of most in vivo-induced genes. Therefore, this study offers important data in the dissection of the transcription regulations in M. tuberculosis, and the strategy should be applicable in the study of DNA-binding factors in a wide range of biological organisms.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\2009\\Genome Research\\Guo et al_2009_Dissecting transcription regulatory pathways through a new bacterial one-hybrid.pdf},
  journal = {Genome Research},
  language = {eng},
  number = {7},
  pmcid = {PMC2704442},
  pmid = {19228590}
}

@article{linBetterUnderstandingAggregation2018,
  ids = {linBetterUnderstandingAggregation2018a},
  title = {Towards a Better Understanding of the Aggregation Mechanisms of Iron (Hydr)Oxide Nanoparticles Interacting with Extracellular Polymeric Substances: {{Role}} of {{pH}} and Electrolyte Solution},
  shorttitle = {Towards a Better Understanding of the Aggregation Mechanisms of Iron (Hydr)Oxide Nanoparticles Interacting with Extracellular Polymeric Substances},
  author = {Lin, Di and Cai, Peng and Peacock, Caroline L. and Wu, Yichao and Gao, Chunhui and Peng, Wanxi and Huang, Qiaoyun and Liang, Wei},
  year = {2018},
  month = dec,
  volume = {645},
  pages = {372--379},
  issn = {0048-9697},
  doi = {10.1016/j.scitotenv.2018.07.136},
  abstract = {Extracellular polymeric substances (EPS) are ubiquitous in the soil and water environment and interact strongly with mineral surfaces. However, these interactions and their impacts on the behavior and fate of minerals remain poorly understood. Here, for a better understanding of the colloidal stability of minerals in the environment, we investigated the aggregation of goethite ({$\alpha$}-FeOOH) nanoparticles (NPs) in the presence of EPS from Bacillus subtilis under different environmental conditions (pH, ionic strength and ionic valence). Results showed that the aggregation processes of goethite NPs are determined by the solution chemistry, and the colloidal stability of goethite NPs is strongly influenced by the addition of EPS. In the absence of ionic strength, the addition of EPS promotes the aggregation of goethite NPs only when the pH (pH = 6) is less than the point of zero charge for the goethite nanoparticles (pHpzc {$\approx$} 8). In the presence of ionic strength, the aggregation rate of goethite NPs increases with increasing concentration of NaCl, NaNO3 and Na2SO4 solutions, and after the addition of EPS solution, the critical coagulation concentrations (CCC) of goethite NPs are increased from 43.0, 56.7 and 0.39 mM to 168.0, 304.9 and 126.2 mM in the three electrolyte solutions, indicating that the addition of EPS inhibits the aggregation of goethite NPs. While in Na3PO4 solution, when the concentration of Na3PO4 solution ranged from 0 to 1 mM, the aggregation rate of goethite NPs increases first, followed by a decrease, and with the concentration of Na3PO4 solution exceeding 1 mM, the aggregation rate of goethite NPs increases again, due to the charge screening by sodium counter ions. This study provides a fundamental understanding of the behavior of goethite NPs in natural soil and water environments.},
  copyright = {All rights reserved},
  journal = {Science of The Total Environment},
  keywords = {课题6研究论文,课题6蔡鹏组},
  language = {en}
}

@article{liSevenFactsFive2020,
  title = {Seven Facts and Five Initiatives for Gut Microbiome Research},
  author = {Li, Danyi and Gao, Chunhui and Zhang, Faming and Yang, Ruifu and Lan, Canhui and Ma, Yonghui and Wang, Jun},
  year = {2020},
  month = jun,
  volume = {11},
  pages = {391--400},
  issn = {1674-8018},
  doi = {10.1007/s13238-020-00697-8},
  file = {E\:\\迅雷下载\\Li2020_Article_SevenFactsAndFiveInitiativesFo.pdf},
  journal = {Protein \& Cell},
  language = {en},
  number = {6}
}

@article{liuSurvivalEscherichiaColi2017,
  ids = {liuSurvivalEscherichiaColi2017a},
  title = {Survival of {{Escherichia}} Coli {{O157}}:{{H7}} in Various Soil Particles: Importance of the Attached Bacterial Phenotype},
  shorttitle = {Survival of {{Escherichia}} Coli {{O157}}},
  author = {Liu, Xing and Gao, Chunhui and Ji, Dandan and Walker, Sharon L. and Huang, Qiaoyun and Cai, Peng},
  year = {2017},
  month = feb,
  volume = {53},
  pages = {209--219},
  issn = {0178-2762},
  doi = {10.1007/s00374-016-1172-y},
  abstract = {The risk of enteropathogens to food and water is highly dependent on their survival in soil environments. Here, the effects of soil type, particle size, the presence of natural organic matter (NOM) or Fe/Al (hydro)oxides on pathogenic Escherichia coli O157:H7 survival in sterilized soil particles were assessed through survival, attachment, metabolic activity, and qRT-PCR analyses. The abundance of inoculated E. coli O157:H7 in Brown soil (Alfisol) particles increased 0.6\textendash 1.4 log10 CFU/g within 3 days (except for NOM-stripped clay), while that in Red soil (Ultisol) particles decreased rapidly in 8 days post-inoculation. Additionally, survival of bacteria was significantly enhanced when Fe/Al (hydro)oxides had been removed from Red soil particles. For the two soils, E. coli O157:H7 survived the longest in NOM-present clays and the bacterial adenosine 5{${'}$}-triphosphate (ATP) levels were 0.7\textendash 2.0 times greater in clays than in sands and silts on day 8. Moreover, clays were more effective than silts and sands in binding cells and changing the expressions of acetate pathway-associated genes (pta and ackA). For silts and sands, E. coli O157:H7 decayed more rapidly in the presence of NOM and similar trends of bacterial ATP levels were observed between NOM-stripped and NOM-present soil particles, indicating that the primary role of NOM was not as a nutrient supply. These findings indicate that soil particles function mainly through attachment to change the metabolic pathway of E. coli O157:H7 and ultimately impact the survival of bacterial pathogens in soils.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\Biology and Fertility of Soils\\2017\\LiuX et al_Biol Fertil Soils_2017.pdf},
  journal = {Biology and Fertility of Soils},
  keywords = {VP引文,课题6研究论文,课题6第一标注,课题6蔡鹏组},
  language = {en},
  number = {2}
}

@article{maBacillusSubtilisBiofilm2017,
  ids = {maBacillusSubtilisBiofilm2017a},
  title = {Bacillus Subtilis Biofilm Development in the Presence of Soil Clay Minerals and Iron Oxides},
  author = {Ma, Wenting and Peng, Donghai and Walker, Sharon L. and Cao, Bin and Gao, Chun-Hui and Huang, Qiaoyun and Cai, Peng},
  year = {2017},
  month = feb,
  volume = {3},
  pages = {4},
  issn = {2055-5008},
  doi = {10.1038/s41522-017-0013-6},
  abstract = {Clay minerals and metal oxides, as important parts of the soil matrix, play crucial roles in the development of microbial communities. However, the mechanism underlying such a process, particularly on the formation of soil biofilm, remains poorly understood. Here, we investigated the effects of montmorillonite, kaolinite, and goethite on the biofilm formation of the representative soil bacteria Bacillus subtilis. The bacterial biofilm formation in goethite was found to be impaired in the initial 24\,h but burst at 48\,h in the liquid\textendash air interface. Confocal laser scanning microscopy showed that the biofilm biomass in goethite was 3\textendash 16 times that of the control, montmorillonite, and kaolinite at 48\,h. Live/Dead staining showed that cells had the highest death rate of 60\% after 4\,h of contact with goethite, followed by kaolinite and montmorillonite. Atomic force microscopy showed that the interaction between goethite and bacteria may injure bacterial cells by puncturing cell wall, leading to the swarming of bacteria toward the liquid\textendash air interface. Additionally, the expressions of abrB and sinR, key players in regulating the biofilm formation, were upregulated at 24\,h and downregulated at 48\,h in goethite, indicating the initial adaptation of the cells to minerals. A model was proposed to describe the effects of goethite on the biofilm formation. Our findings may facilitate a better understanding of the roles of soil clays in biofilm development and the manipulation of bacterial compositions through controlling the biofilm in soils. The effect of three soil minerals on biofilm production is clarified by research using the common soil bacterium Bacillus subtilis. The mineral composition of soil is known to affect biofilm production, but the mechanisms underpinning minerals' influences have not been well studied. Peng Cai and colleagues at Huazhong Agricultural University in China, with co-workers in the United States and Singapore, studied Bacillus subtilis growing in the presence of the minerals montmorillonite, kaolinite, and goethite. Their results suggest the minerals, especially goethite, can encourage biofilm formation by promoting the bursting of bacterial cells. The effect of goethite was attributed to the size of its grains being generally smaller than the bacterial cells. By quantifying the effect of these minerals, the research will assist understanding of biofilm formation and the growth and persistence of bacterial populations in soils.},
  copyright = {2017 The Author(s)},
  file = {E\:\\zotero.storage.2016\\npj Biofilms and Microbiomes\\2017\\MaW et al_2017.pdf},
  journal = {npj Biofilms and Microbiomes},
  keywords = {课题6研究论文,课题6蔡鹏组},
  language = {En},
  number = {1}
}

@article{ouyangEffectsHumicAcid2017,
  ids = {ouyangEffectsHumicAcid2017a},
  title = {Effects of Humic Acid on the Interactions between Zinc Oxide Nanoparticles and Bacterial Biofilms},
  author = {Ouyang, Kai and Yu, Xiao-Ying and Zhu, Yunlin and Gao, Chunhui and Huang, Qiaoyun and Cai, Peng},
  year = {2017},
  month = aug,
  volume = {231},
  pages = {1104--1111},
  issn = {0269-7491},
  doi = {10.1016/j.envpol.2017.07.003},
  abstract = {The effects of humic acid (HA) on interactions between ZnO nanoparticles (ZnO NPs) and Pseudomonas putida KT2440 biofilms at different maturity stages were investigated. Three stages of biofilm development were identified according to bacterial adenosine triphosphate (ATP) activity associated with biofilm development process. In the initial biofilm stage 1, the ATP content of bacteria was reduced by more than 90\% when biofilms were exposed to ZnO NPs. However, in the mature biofilm stages 2 and 3, the ATP content was only slightly decreased. Biofilms at stage 3 exhibited less susceptibility to ZnO NPs than biofilms at stage 2. These results suggest that more mature biofilms have a significantly higher tolerance to ZnO NPs compared to young biofilms. In addition, biofilms with intact extracellular polymeric substances (EPS) showed higher tolerance to ZnO NPs than those without EPS, indicating that EPS play a key role in alleviating the toxic effects of ZnO NPs. In both pure ZnO NPs and ZnO-HA mixtures, dissolved Zn2+ originating from the NPs significantly contributed to the overall toxicity. The presence of HA dramatically decreased the toxicity of ZnO NPs due to the binding of Zn2+ on HA. The combined results from this work suggest that the biofilm maturity stages and environmental constituents (such as humic acid) are important factors to consider when evaluating potential risks of NPs to ecological systems.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\Environmental Pollution\\2017\\OuyangK et al_Environmental Pollution_2017.pdf},
  journal = {Environmental Pollution},
  keywords = {课题6研究论文,课题6蔡鹏组},
  number = {1}
}

@article{ouyangMetabolismSurvivalGene2018,
  title = {Metabolism, Survival, and Gene Expression of {{Pseudomonas}} Putida to Hematite Nanoparticles Mediated by Surface-Bound Humic Acid},
  author = {Ouyang, Kai and Walker, Sharon L. and Yu, Xiao-Ying and Gao, Chun-Hui and Huang, Qiaoyun and Cai, Peng},
  year = {2018},
  month = mar,
  volume = {5},
  pages = {682--695},
  doi = {10.1039/c7en01039g},
  abstract = {Natural organic matter (NOM) is likely to coat nanoparticles (NPs) in the environment and poses distinct effects on the viability of microorganisms. However, such a topic has not been well investigated; hence, this study was designed to explore the interactions of NOM, NPs, and bacteria in a model system and, specifically, the influence of surface-bound humic acid (HA) on the toxicity of hematite NPs to Pseudomonas putida. Results showed that pure hematite NPs could inhibit the bacterial growth with a median lethal concentration (24 h LC50) of 23.58 mg L-1, while surface-bound HA could significantly mitigate the toxicity of hematite with the highest LC50 of 4774.23 mg L-1, which were corroborated by the transcriptional regulation of Pseudomonas putida cell activity-related genes. Co-precipitation experiments and transmission electron microscopy observations revealed that surfacebound HA prevented the adhesion of hematite to the cells and limited cell internalization. Compared to hematite NPs, the generation of intracellular reactive oxygen species (ROS) and the expression of oxidative stress genes were significantly inhibited in hematite surface-bound HA systems. The prevention of adhesion and inhibition of ROS production could account for the HA-mitigated nanotoxicity. Interfacial interactions between hematite and bacteria were also evaluated on the basis of the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, suggesting that the more adhesive conditions resulted in greater toxicity and the more repulsive conditions resulted in a reduced toxicity of the model microorganism. The results of this study serve as a platform to better understand the interactions between bacteria or bacterial biofilms and minerals in the natural environment.},
  annotation = {WOS:000435961700006},
  file = {E\:\\zotero.storage.2016\\2018\\Environmental Science Nano\\Ouyang et al_2018_Metabolism, survival, and gene expression of Pseudomonas putida to hematite.pdf},
  journal = {Environmental Science-Nano},
  keywords = {课题6研究论文,课题6蔡鹏组},
  number = {3}
}

@article{ouyangMetalfreeInactivationColi2017,
  ids = {ouyangMetalfreeInactivationColi2017a},
  title = {Metal-Free Inactivation of {{E}}. Coli {{O157}}:{{H7}} by Fullerene/{{C3N4}} Hybrid under Visible Light Irradiation},
  shorttitle = {Metal-Free Inactivation of {{E}}. Coli {{O157}}},
  author = {Ouyang, Kai and Dai, Ke and Chen, Hao and Huang, Qiaoyun and Gao, Chunhui and Cai, Peng},
  year = {2017},
  month = feb,
  volume = {136},
  pages = {40--45},
  issn = {0147-6513},
  doi = {10.1016/j.ecoenv.2016.10.030},
  abstract = {Interest has grown in developing safe and high-performance photocatalysts based on metal-free materials for disinfection of bacterial pathogens under visible light irradiation. In this paper, the C60/C3N4 and C70/C3N4 hybrids were synthesized by a hydrothermal method, and characterized by X-ray diffraction (XRD), UV-vis diffuse reflection spectroscopy (UV\textendash vis DRS), Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), and high revolution transmission electron microscope (HRTEM). The performance of photocatalytic disinfection was investigated by the inactivation of Escherichia coli O157:H7. Both C60/C3N4 and C70/C3N4 hybrids showed similar crystalline structure and morphology with C3N4; however, the two composites exhibited stronger bacterial inactivation than C3N4. In particular, C70/C3N4 showed the highest bactericidal efficiency and was detrimental to all E. coli O157:H7 in 4 h irradiation. Compared to C3N4, the enhancement of photocatalytic activity of composites could be attributed to the effective transfer of the photoinduced electrons under visible light irradiation. Owing to the excellent performance of fullerenes (C60, C70)/C3N4 composites, a visible light response and environmental friendly photocatalysts for disinfection were achieved.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\Ecotoxicology and Environmental Safety\\2017\\OuyangK et al_Ecotoxicology and Environmental Safety_2017.pdf},
  journal = {Ecotoxicology and Environmental Safety},
  keywords = {课题6研究论文,课题6蔡鹏组}
}

@article{pengExopolysaccharideeDNAInteractionModulates2020,
  title = {The Exopolysaccharide-{{eDNA}} Interaction Modulates {{3D}} Architecture of {{Bacillus}} Subtilis Biofilm},
  author = {Peng, Na and Cai, Peng and Mortimer, Monika and Wu, Yichao and Gao, Chunhui and Huang, Qiaoyun},
  year = {2020},
  month = may,
  volume = {20},
  pages = {115},
  doi = {10.1186/s12866-020-01789-5},
  abstract = {Background Bacterial biofilms are surface-adherent microbial communities in which individual cells are surrounded by a self-produced extracellular matrix of polysaccharides, extracellular DNA (eDNA) and proteins. Interactions among matrix components within biofilms are responsible for creating an adaptable structure during biofilm development. However, it is unclear how the interactions among matrix components contribute to the construction of the three-dimensional (3D) biofilm architecture. Results DNase I treatment significantly inhibited Bacillus subtilis biofilm formation in the early phases of biofilm development. Confocal laser scanning microscopy (CLSM) and image analysis revealed that eDNA was cooperative with exopolysaccharide (EPS) in the early stages of B. subtilis biofilm development, while EPS played a major structural role in the later stages. In addition, deletion of the EPS production gene epsG in B. subtilis SBE1 resulted in loss of the interaction between EPS and eDNA and reduced the biofilm biomass in pellicles at the air-liquid interface. The physical interaction between these two essential biofilm matrix components was confirmed by isothermal titration calorimetry (ITC). Conclusions Biofilm 3D structures become interconnected through surrounding eDNA and EPS. eDNA interacts with EPS in the early phases of biofilm development, while EPS mainly participates in the maturation of biofilms. The findings of this study provide a better understanding of the role of the interaction between eDNA and EPS in shaping the biofilm 3D matrix structure and biofilm formation.},
  annotation = {WOS:000536241700001},
  journal = {Bmc Microbiology},
  keywords = {课题6研究论文,课题6蔡鹏组},
  number = {1}
}

@article{sunZiRanHuanJingZhongDeDuoWuZhongShengWuMoYanJiuFangFaJiSheQunXiangHuZuoYong2017,
  title = {自然环境中的多物种生物膜:研究方法及社群相互作用},
  shorttitle = {自然环境中的多物种生物膜},
  author = {孙, 晓洁 and 高, 春辉 and 黄, 巧云 and 蔡, 鹏},
  year = {2017},
  pages = {6--14},
  abstract = {自然界中的微生物大多以多物种生物膜的形式存在,这种生命形式可以增加微生物对外界环境胁迫的耐受性。在多物种生物膜中,微生物之间的相互作用包括合作、竞争、信号分子的传递、以及水平基因转移等。研究自然环境中多物种生物膜内部微生物之间的相互作用,不仅对于理解自然生物膜的形成和演替过程具有重要意义,而且也可以为多物种生物膜在环境质量提升、微生物多样性维持等方面提供理论指导。本文主要分为两个部分:第一部分总结了环境中多物种生物膜的研究方法,包括实验室模拟体系下生物膜的构建及其分析检测技术;第二部分论述了天然多物种生物膜内细菌间的相互作用。},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\农业资源与环境学报\\2017\\孙晓 et al_2017.pdf},
  journal = {农业资源与环境学报},
  keywords = {课题6研究论文,课题6第一标注,课题6蔡鹏组},
  number = {01}
}

@article{wangDaChangGanJunBiaoMianGanYingJiZhiYanJiuJinZhan2017,
  ids = {liliangResearchProgressMechanism2017},
  title = {{大肠杆菌表面感应机制研究进展}},
  author = {王, 立亮 and 高, 春辉 and 吴, 一超 and 黄, 巧云 and 蔡, 鹏},
  year = {2017},
  volume = {43},
  pages = {685--690},
  issn = {1008-9209},
  abstract = {大肠杆菌是人和动物胃肠道的主要兼性厌氧菌群,既能在宿主体内生存,也能吸附在环境中的固体介质表面形成生物膜而得以存活和传播。吸附是生物膜形成的关键,它能改变细胞运动性和代谢等相关基因的表达,进而影响细胞的性质和行为。细菌对表面的"感知"以及初始吸附后细胞的"响应"过程统称为"表面感应"。对细菌表面感应机制的研究有助于我们加深对微生物尤其是病原菌在土壤环境中的存活和迁移,以及土壤生物膜形成过程的理解。本文结合多种微生物表面感应的研究进展,阐述了表面感应的概念,重点关注了近期有关大肠杆菌表面感应的研究,并对未来工作进行了展望。},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\2017\\浙江大学学报(农业与生命科学版)\\王 et al_2017_大肠杆菌表面感应机制研究进展.pdf},
  journal = {浙江大学学报(农业与生命科学版)},
  keywords = {课题6研究论文,课题6第一标注,课题6蔡鹏组},
  language = {中文;},
  lccn = {33-1247/S},
  number = {6}
}

@article{wangExtractionExtracellularPolymeric2019,
  ids = {wangExtractionExtracellularPolymeric2019a},
  title = {Extraction of Extracellular Polymeric Substances ({{EPS}}) from Red Soils ({{Ultisols}})},
  author = {Wang, Shuang and {Redmile-Gordon}, Marc and Mortimer, Monika and Cai, Peng and Wu, Yichao and Peacock, Caroline L. and Gao, Chunhui and Huang, Qiaoyun},
  year = {2019},
  month = aug,
  volume = {135},
  pages = {283--285},
  issn = {0038-0717},
  doi = {10.1016/j.soilbio.2019.05.014},
  abstract = {Extracellular polymeric substances (EPS) have many beneficial functions in soils. Accurate quantification of EPS in soils is crucial. Here, five methods were compared for their suitability for extraction of EPS from Ultisols: hot water extractable polysaccharide (HWEP), hot dilute acid extractable polysaccharide (HDAEP), easily extractable glomalin (EEG), sodium sulfide (SS) and cation exchange resin (CER) method. Humic-acid equivalent (HAE) was used as an indicator for extracellular contamination and ATP for quantifying intracellular contamination from cell lysis. Among the tested methods, CER resulted in EPS extraction with minimal contamination. Therefore, we propose that CER is currently the most appropriate method for extraction of EPS from Ultisols.},
  copyright = {All rights reserved},
  file = {C\:\\Users\\gaoch\\Zotero\\storage\\WJPPC6TC\\Wang et al_2019_Extraction of extracellular polymeric substances (EPS) from red soils (Ultisols).pdf},
  journal = {Soil Biology and Biochemistry},
  keywords = {课题6研究论文,课题6蔡鹏组},
  language = {en}
}

@article{wangGlobalProteinProtein2010,
  title = {Global {{Protein}}-{{Protein Interaction Network}} in the {{Human Pathogen Mycobacterium}} Tuberculosis {{H37Rv}}},
  author = {Wang, Yi and Cui, Tao and Zhang, Cong and Yang, Min and Huang, Yuanxia and Li, Weihui and Zhang, Lei and Gao, Chunhui and He, Yang and Li, Yuqing and Huang, Feng and Zeng, Jumei and Huang, Cheng and Yang, Qiong and Tian, Yuxi and Zhao, Chunchao and Chen, Huanchun and Zhang, Hua and He, Zheng-Guo},
  year = {2010},
  month = dec,
  volume = {9},
  pages = {6665--6677},
  issn = {1535-3893},
  doi = {10.1021/pr100808n},
  abstract = {Analysis of the protein-protein interaction network of a pathogen is a powerful approach for dissecting gene function, potential signal transduction, and virulence pathways. This study looks at the construction of a global protein-protein interaction (PPI) network for the human pathogen Mycobacterium tuberculosis H37Rv, based on a high-throughput bacterial two-hybrid method. Almost the entire ORFeome was cloned, and more than 8000 novel interactions were identified. The overall quality of the PPI network was validated through two independent methods, and a high success rate of more than 60\% was obtained. The parameters of PPI networks were calculated. The average shortest path length was 4.31. The topological coefficient of the M. tuberculosis B2H network perfectly followed a power law distribution (correlation = 0.999; R-squared = 0.999) and represented the best fit in all currently available PPI networks. A cross-species PPI network comparison revealed 94 conserved subnetworks between M. tuberculosis and several prokaryotic organism PPI networks. The global network was linked to the protein secretion pathway. Two WhiB-like regulators were found to be highly connected proteins in the global network. This is the first systematic noncomputational PPI data for the human pathogen, and it provides a useful resource for studies of infection mechanisms, new signaling pathways, and novel antituberculosis drug development.},
  copyright = {All rights reserved},
  journal = {Journal of Proteome Research},
  number = {12}
}

@article{wuRecentAdvancesMicrobial2018,
  ids = {wuRecentAdvancesMicrobial2018a},
  title = {Recent Advances in Microbial Electrochemical System for Soil Bioremediation},
  author = {Wu, Yichao and Jing, Xinxin and Gao, Chunhui and Huang, Qiaoyun and Cai, Peng},
  year = {2018},
  month = nov,
  volume = {211},
  pages = {156--163},
  issn = {0045-6535},
  doi = {10.1016/j.chemosphere.2018.07.089},
  abstract = {Soil contamination poses a serious threat to ecosystem and human well-being. Compared to conventional physical and chemical treatment, the microbial electrochemical system (MES) offers a sustainable and environment-friendly solution for soil bioremediation. In principle, soil microbe degrades organic substrate and releases electron in anode region. The electron flows through electric circuit to the cathode and finally is accepted by oxygen or oxidized metals. With various inherent advantages, MES has been applied in petroleum hydrocarbon, chlorinated organics and heavy metals bioremediation in soils. This paper aims to review the recent advances of MES in soil bioremediation, including main mechanisms of contaminant removal with MES, configurations of soil MES and current development in bioremediation of soil contaminated by organic and inorganic pollutants. Moreover, challenges and future prospects of soil MES are discussed.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\2018\\Chemosphere\\Wu et al_2018_Recent advances in microbial electrochemical system for soil bioremediation.pdf},
  journal = {Chemosphere},
  keywords = {课题6研究论文,课题6蔡鹏组}
}

@article{wuSoilBiofilmFormation2019,
  ids = {wuSoilBiofilmFormation2019a},
  title = {Soil Biofilm Formation Enhances Microbial Community Diversity and Metabolic Activity},
  author = {Wu, Yichao and Cai, Peng and Jing, Xinxin and Niu, Xueke and Ji, Dandan and Ashry, Noha Mohamed and Gao, Chunhui and Huang, Qiaoyun},
  year = {2019},
  month = nov,
  volume = {132},
  pages = {105116},
  issn = {0160-4120},
  doi = {10.1016/j.envint.2019.105116},
  abstract = {Biofilms have been extensively studied in aquatic and clinical environments. However, the complexity of edaphic microenvironment hinders the advances toward understanding the environmental functionalities and ecological roles of soil biofilms. In this work, artificial soil was employed to investigate the soil biofilm formation and corresponding impacts on community structure and microbial activities. Our results showed that extracellular polymeric substances (EPS) production was significantly enhanced and micro-meter sized cell aggregates formed with high glucose amendment. Biofilm development exhibited significant effects on the soil microbial processes. 16S rRNA gene sequencing demonstrated the soils with biofilms and free-living cells shared similar microbial communities. But the Shannon diversity and evenness indices of communities with soil biofilms were significantly enhanced by 18.2\% and 17.1\%. The soil with biofilms also revealed a rapid response to nutrient provision and robust microbial activity, which consumed 65.4\% more oxygen in the topsoil (0\textendash 1.5 mm). Kinetic respiration analysis showed that the enhanced metabolic activity was attributed to 23-times more active microbes in soil biofilms. In summary, this study revealed that soil biofilms can sustain a diverse and robust community to drive soil biogeochemical processes.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\2019\\Environment International\\Wu et al_2019_Soil biofilm formation enhances microbial community diversity and metabolic.pdf},
  journal = {Environment International},
  keywords = {课题6研究论文,课题6蔡鹏组}
}

@article{yangCdIIBinding2021,
  ids = {yangCdIIBinding2020},
  title = {Cd({{II}})-Binding Transcriptional Regulator Interacts with Isoniazid and Regulates Drug Susceptibility in Mycobacteria},
  author = {Yang, Min and Jia, Shi-Hua and Tao, Hui-Ling and Zhu, Chen and Jia, Wan-Zhong and Hu, Li-Hua and Gao, Chun-Hui},
  year = {2021},
  month = feb,
  volume = {169},
  pages = {43--53},
  issn = {1756-2651},
  doi = {10.1093/jb/mvaa086},
  abstract = {It is urgent to understand the regulatory mechanism of drug resistance in widespread bacterial pathogens. In Mycobacterium tuberculosis, several transcriptional regulators have been found to play essential roles in regulating its drug resistance. In this study, we found that an ArsR family transcription regulator encoded by Rv2642 (CdiR) responds to isoniazid (INH), a widely used anti-tuberculosis (TB) drug. CdiR negatively regulates self and adjacent genes, including arsC (arsenic-transport integral membrane protein ArsC). CdiR directly interacts with INH and Cd(II). The binding of INH and Cd(II) both reduce its DNA-binding activity. Disrupting cdiR increased the drug susceptibility to INH, whereas overexpressing cdiR decreased the susceptibility. Strikingly, overexpressing arsC increased the drug susceptibility as well as cdiR. Additionally, both changes in cdiR and arsC expression caused sensitivity to other drugs such as rifamycin and ethambutol, where the minimal inhibitory concentrations in the cdiR deletion strain were equal to those of the arsC-overexpressing strain, suggesting that the function of CdiR in regulating drug resistance primarily depends on arsC. Furthermore, we found that Cd(II) enhances bacterial resistance to INH in a CdiR-dependent manner. As a conclusion, CdiR has a critical role in directing the interplay between Cd(II) metal ions and drug susceptibility in mycobacteria.},
  file = {C\:\\Users\\gaoch\\Zotero\\storage\\GG6PK9BH\\Yang et al_2020_Cd(II)-binding transcriptional regulator interacts with isoniazid and regulates.pdf},
  journal = {Journal of Biochemistry},
  keywords = {高春辉一作或通讯论文},
  language = {eng},
  number = {1},
  pmid = {32706888}
}

@article{yangCharacterizationInteractionCrossRegulation2010,
  title = {Characterization of the {{Interaction}} and {{Cross}}-{{Regulation}} of {{Three Mycobacterium}} Tuberculosis {{RelBE Modules}}},
  author = {Yang, Min and Gao, Chunhui and Wang, Yi and Zhang, Hua and He, Zheng-Guo},
  year = {2010},
  month = may,
  volume = {5},
  pages = {e10672},
  issn = {1932-6203},
  doi = {10.1371/journal.pone.0010672},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\PLoS ONE\\2010\\2010_Characterization of the Interaction and Cross-Regulation of Three Mycobacterium tuberculosis RelBE Modules_2.pdf},
  journal = {PLoS ONE},
  language = {en},
  number = {5}
}

@article{yangCharacterizationInteractionSirR2014,
  title = {Characterization of the Interaction between a {{SirR}} Family Transcriptional Factor of {{Mycobacterium}}~Tuberculosis, Encoded by {{Rv2788}}, and a Pair of Toxin-Antitoxin Proteins {{RelJ}}/{{K}}, Encoded by {{Rv3357}} and {{Rv3358}}},
  author = {Yang, Min and Gao, Chun-Hui and Hu, Jialing and Dong, Chao and He, Zheng-Guo},
  year = {2014},
  month = jun,
  volume = {281},
  pages = {2726--2737},
  issn = {1742-4658},
  doi = {10.1111/febs.12815},
  abstract = {Toxin-antitoxin (TA) systems play significant roles in the regulation of bacterial growth and persistence, and their functions usually depend on protein-protein interaction between their constituent TA proteins. However, the regulatory mechanisms of these systems, particularly their interaction with other cellular components, are still poorly understood. This study investigated cross-talk between the TA module RelJ/K (Rv3357/Rv3358) and the transcriptional regulator staphylococcal iron regulator repressor (SirR, Rv2788) from Mycobacterium~tuberculosis. We characterized the physical interaction of SirR with both RelJ and RelK using bacterial two-hybrid, pull-down and co-immunoprecipitation assays. Similarly to RelK, SirR regulates the DNA-binding activity of RelJ and alleviates its inhibitory effect on the activity of the Rv3357p promoter. Furthermore, SirR may replace RelJ to alleviate the inhibitory effect of the toxin RelK on bacterial growth. Conversely, both RelJ and RelK competitively inhibit the interaction between SirR and their respective promoters. Thus, our results show that SirR interacts with a pair of toxin and antitoxin proteins, and exhibits antitoxin-like function to neutralize the toxin. These findings demonstrate a novel function of the SirR regulator of M.~tuberculosis as well as a novel mechanism of regulation of TA systems. STRUCTURED DIGITAL ABSTRACT: SirR~binds~to~RelJ~by~pull down~(view interaction) SirR~binds to RelK by pull down (view interaction) RelJ~physically interacts with RelK by anti bait coimmunoprecipitation (1, 2) SirR~physically interacts with RelK by anti bait coimmunoprecipitation (view interaction) SirR~physically interacts with RelJ by anti bait coimmunoprecipitation (view interaction) RelJ and SirR~physically interact by two-hybrid (view interaction) SirR and RelK~physically interact by two-hybrid (view interaction) RelK and RelJ~physically interact by two-hybrid (view interaction).},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\The FEBS journal\\2014\\FEBS J._2014_Characterization of the interaction between a SirR family transcriptional factor of Mycobacterium tuberculosis, encoded by Rv2788, and a pair of.pdf},
  journal = {The FEBS journal},
  language = {eng},
  number = {12},
  pmid = {24725376}
}

@article{yangInbRTetRFamily2015,
  title = {{{InbR}}, a {{TetR}} Family Regulator, Binds with Isoniazid and Influences Multidrug Resistance in {{Mycobacterium}} Bovis {{BCG}}},
  author = {Yang, Min and Gao, Chun-Hui and Hu, Jialing and Zhao, Lei and Huang, Qiaoyun and He, Zheng-Guo},
  year = {2015},
  month = sep,
  volume = {5},
  pages = {13969},
  issn = {2045-2322},
  doi = {10.1038/srep13969},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\Scientific Reports\\2015\\2015_InbR, a TetR family regulator, binds with isoniazid and influences multidrug resistance in Mycobacterium bovis BCG_2.pdf},
  journal = {Scientific Reports},
  keywords = {杨敏2016年面上项目}
}

@article{yangOxiRSpecificallyResponds2019,
  title = {{{OxiR}} Specifically Responds to Isoniazid and Regulates Isoniazid Susceptibility in Mycobacteria},
  author = {Yang, Min and Zhang, Li and Tao, Hui-Ling and Sun, Yuan-Chao and Lou, Zhong-Zi and Jia, Wan-Zhong and Hu, Li-Hua and Gao, Chun-Hui},
  year = {2019},
  month = may,
  volume = {366},
  publisher = {{Oxford Academic}},
  issn = {1574-6968},
  doi = {10.1093/femsle/fnz109},
  abstract = {The bacteria drug resistance is not only associated with the gain of drug resistance gene but also relied on the adaptation of bacterial cells to antibiotics by transcriptional regulation. However, only a few transcription factors that regulate drug resistance have been characterized in mycobacteria. In this study, a TetR family transcriptional factor (OxiR), encoded by Rv0067c in Mycobacterium tuberculosis, was found to be an isoniazid (INH) resistance regulator. Comparing with the wild-type strain, the oxiR overexpressing strain is four times resistant to INH, whereas the oxiR knockout strain is eight times sensitive to INH. However, the rifamycin and ethambutol resistance were not influenced by oxiR. OxiR can bind to self-promoter at a 66 bp imperfect palindromic motifs. Interestingly, OxiR directly binds to INH, and thereby alleviate the self-repression. Furthermore, OxiR negatively regulated an oxidoreductase encoded by Rv0068. And the susceptibility of the Rv0068-overexpressing and oxiR knockout strains to all the three above-mentioned anti-tuberculosis drugs was equivalent, suggesting that the effect of oxiR to INH susceptibility is attributed to the derepression of Rv0068. In conclusion, we showed that OxiR can specifically modulate INH susceptibility by regulating an oxidoreductase encoding gene, both of which have not been associated with drug-resistance previously.},
  file = {C\:\\Users\\gaoch\\Zotero\\storage\\PV38RHJR\\Yang et al_2019_OxiR specifically responds to isoniazid and regulates isoniazid susceptibility.pdf},
  journal = {FEMS microbiology letters},
  keywords = {高春辉一作或通讯论文},
  language = {eng},
  number = {10},
  pmid = {31125044}
}

@article{yangTetRlikeRegulatorBroadly2012,
  title = {A {{TetR}}-like Regulator Broadly Affects the Expressions of Diverse Genes in {{Mycobacterium}} Smegmatis},
  author = {Yang, Min and Gao, Chunhui and Cui, Tao and An, Jingning and He, Zheng-Guo},
  year = {2012},
  month = feb,
  volume = {40},
  pages = {1009--1020},
  issn = {0305-1048, 1362-4962},
  doi = {10.1093/nar/gkr830},
  abstract = {Transcriptional regulation plays a critical role in the life cycle of Mycobacterium smegmatis and its related species, M. tuberculosis, the causative microbe for tuberculosis. However, the key transcriptional factors involved in broad regulation of diverse genes remain to be characterized in mycobacteria. In the present study, a TetR-like family transcriptional factor, Ms6564, was characterized in M. smegmatis as a master regulator. A conserved 19 bp-palindromic motif was identified for Ms6564 binding using DNaseI footprinting and EMSA. A total of 339 potential target genes for Ms6564 were further characterized by searching the M. smegmatis genome based on the sequence motif. Notably, Ms6564 bound with the promoters of 37 cell cycle and DNA damage/repair genes and regulated positively their expressions. The Ms6564-overexpressed recombinant strain yielded 5-fold lower mutation rates and mutation frequencies, whereas deletion of Ms6564 resulted in {$\sim$}5-fold higher mutation rates for the mutant strain compared with the wild-type strain. These findings suggested that Ms6564 may function as a global regulator and might be a sensor necessary for activation of DNA damage/repair genes.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\Nucleic Acids Research\\2012\\Nucl. Acids Res._2012_A TetR-like regulator broadly affects the expressions of diverse genes in Mycobacterium smegmatis.pdf},
  journal = {Nucleic Acids Research},
  language = {en},
  number = {3},
  pmid = {21976733}
}

@article{zhangArchaealEukaryotelikeOrc12009,
  title = {Archaeal Eukaryote-like {{Orc1}}/{{Cdc6}} Initiators Physically Interact with {{DNA}} Polymerase {{B1}} and Regulate Its Functions},
  author = {Zhang, Lu and Zhang, Lei and Liu, Yi and Yang, Shifan and Gao, Chunhui and Gong, Hongchao and Feng, Ying and He, Zheng-Guo},
  year = {2009},
  month = may,
  volume = {106},
  pages = {7792--7797},
  issn = {0027-8424, 1091-6490},
  doi = {10.1073/pnas.0813056106},
  abstract = {Archaeal DNA replication machinery represents a core version of that found in eukaryotes. However, the proteins essential for the coordination of origin selection and the functioning of DNA polymerase have not yet been characterized in archaea, and they are still being investigated in eukaryotes. In the current study, the Orc1/Cdc6 (SsoCdc6) proteins from the crenarchaeon Sulfolobus solfataricus were found to physically interact with its DNA polymerase B1 (SsoPolB1). These SsoCdc6 proteins stimulated the DNA-binding ability of SsoPolB1 and differentially regulated both its polymerase and nuclease activities. Furthermore, the proteins also mutually regulated their interactions with SsoPolB1. In addition, SsoPolB1c467, a nuclease domain-deleted mutant of SsoPolB1 defective in DNA binding, retains the ability to physically interact with SsoCdc6 proteins. Its DNA polymerase activity could be stimulated by these proteins. We report on a linkage between the initiator protein Orc1/Cdc6 and DNA polymerase in the archaeon. Our present and previous findings indicate that archaeal Orc1/Cdc6 proteins could potentially play critical roles in the coordination of origin selection and cell-cycle control of replication.},
  copyright = {\textcopyright{} 2009},
  journal = {Proceedings of the National Academy of Sciences},
  language = {en},
  number = {19},
  pmid = {19416914}
}

@article{zhangNovelMarRABOperon2014,
  title = {A {{Novel marRAB Operon Contributes}} to the {{Rifampicin Resistance}} in {{Mycobacterium}} Smegmatis},
  author = {Zhang, Haiwei and Gao, Long and Zhang, Jiaoling and Li, Weihui and Yang, Min and Zhang, Hua and Gao, Chunhui and He, Zheng-Guo},
  year = {2014},
  month = aug,
  volume = {9},
  pages = {e106016},
  doi = {10.1371/journal.pone.0106016},
  abstract = {The multiple-antibiotic resistance regulator (MarR) plays an important role in modulating bacterial antibiotic resistance. However, the regulatory model of the marRAB operon in mycobacteria remains to be characterized. Here we report that a MarR, encoded by Ms6508, and its marRAB operon specifically contribute to rifampicin (RIF) resistance in Mycobacterium smegmatis. We show that the MarR recognizes a conserved 21-bp palindromic motif and negatively regulates the expression of two ABC transporters in the operon, encoded by Ms6509\textendash 6510. Unlike other known drug efflux pumps, overexpression of these two ABC transporters unexpectedly increased RIF sensitivity and deletion of these two genes increased mycobacterial resistance to the antibiotic. No change can be detected for the sensitivity of recombinant mycobacterial strains to three other anti-TB drugs. Furthermore, HPLC experiments suggested that Ms6509\textendash Ms6510 could pump RIF into the mycobacterial cells. These findings indicated that the mycobacterial MarR functions as a repressor and constitutively inhibits the expression of the marRAB operon, which specifically contributes to RIF resistance in M. smegmatis. Therefore, our data suggest a new regulatory mechanism of RIF resistance and also provide the new insight into the regulatory model of a marRAB operon in mycobacteria.},
  copyright = {All rights reserved},
  file = {E\:\\zotero.storage.2016\\PLoS ONE\\2014\\PLoS ONE_2014_A Novel marRAB Operon Contributes to the Rifampicin Resistance in Mycobacterium smegmatis.pdf},
  journal = {PLoS ONE},
  number = {8}
}


